Ch. 2: Amino acids and proteins
1. Why do amino acids, when dissolved in water, become
zwitterions?
2. The amino acid histidine has a side chain for which the
pKa is 6.0. Calculate what fraction of the histidine side chains will carry a
positive charge at pH 5.4.
3. The hydrophobic effect makes an important energetic
contribution to:
A. membrane structure.
B. protein tertiary structure.
C. protein quartenary structure.
D. enzyme-substrate interactions.
E. all of the above.
4. How many peptide bonds are in an octapeptide?
5. In the isoelectric form of a tetrapeptide:
A. the amino and carboxyl termini are not charged.
B. two internal amino acids of the tetrapeptide cannot have
ionizable R groups.
C. the total net charge is zero.
D. there are four ionic charges.
E. only the amino and carboxyl termini contribute charge.
6. How can a polypeptide have only one free amino group and one
free
carboxyl group?
7. Except for glycine, the side chains of nonpolar amino acids are
best categorized:
A. as ring structures.
B. as organic bases with a positive charge.
C. as organic acids with a negative charge.
D. as neutral hydrocarbon structures.
E. by the presence of a hydroxyl, carboxyl, or sulfur-containing
group.
8. For amino acids with neutral R groups, at any pH below
the pI of
the amino acid, the population of amino acids in solution will:
A. be neutral without any charge.
B. show no net charge.
C. have a net positive charge.
D. have positive and negative charges in equal concentration.
E. have a net negative charge.
9. Give the general Henderson-Hasselbalch equation and sketch the
plot it describes (pH against amount of NaOH added to a weak
acid).
On your curve label the pKa for the weak acid, and indicate the
region in which the buffering capacity of the system is greatest.
10. What are buffers? Write two characteristics of buffers.
11. Draw the structures of Ala and Gly in the ionization state you
would expect at pH 7.0.
12. For a weak acid with a pKa of 6.0, show how you would
calculate the ratio of acid to salt at pH 5.
13. Name and briefly define four types of noncovalent
interactions that occur between biological molecules.
14. How does an oligopeptide differ from a polypeptide?
15. What amino acid characteristics can be used to detect
proteins by the absorbance of ultraviolet light?
16. Aspartate is very soluble in water; phenylalanine is much less
soluble in water. In two or three sentences, explain this difference in
solubility.
17. The peptide alanylglutamylglycylalanylleucine has:
A. four peptide bonds.
B. two free amino groups.
C. a disulfide bridge.
D. no free carboxyl group.
E. five peptide bonds.
18. In a highly basic solution, pH = 13, the dominant form of
glycine is:
A. NH2-CH2-COOH.
B. NH3+-CH2-COOH.
C. NH2-CH2-COO-.
D. NH3+-CH2-COO-.
E. NH2-CH3+-COO-.
19. What are the structural characteristics common to all amino
acids found in naturally occurring proteins?
20. Briefly describe the five major groupings of amino acids.
21. Which one of the 20 amino acids is not really an amino acid?
22. Write names of the amino acids, which are potential targets of
phosphorylation.
23. What do
you mean by the statement "amino acids are amphoteric molecules"?
24. What is
"domain" in a protein? Is it one of the four types of structures of
proteins?
25. Other
than the four non-covalent interactions, which interaction helps stabilize
tertiary and quaternary structures of proteins?
26. Which
amino acids do usually participate in beta-turn/bend in the secondary structure
of proteins?
1. All enzymes are proteins. (Yes/No)
2. The enzymes are different from inorganic catalysts in
................
3. The enzymes are specific in two ways: ..................... and
(2) ....................
4. The conversion of threonine to isoleucine is regulated by
feed-back inhibition. In this mechanism, the product binds on the catalytic
site of the enzyme and stops the reaction (True/False). Give reasons.
5. Write down the types of enzymes which are involved in
phosphorylation and dephosphorylation process, a regulatory mechanism of enzyme
activities.
6. Define zymogens with two examples.
7. Does free energy of ground state of the reactants or the
products affect the velocity of the reaction?
8. Do enzymes catalyze the reaction by altering the equilibrium?
9. Name the types of interactions involved in ES complex
formation.
10.Which one is more stable, S (substrate) or S (transition
state)?
11. Write down the Michaelis-Menton equation and define various
terms in it (V, Vmax and Km).
12. At low [S], the recation velocity is dependent/independent of
substrate.
13. List two differences between the enzymes which obey
Michaelis-Menton equation and the allosterically regulated enzymes.
14. What is the benefits of Lineweaver-Burk plot over hyperbolic
curve?
15. Km is a determinant of the substrate affinity?
16. What is the fate of an enzyme once the recation is complete?
17. Nerve gas produces ...................... type of inhibition
in acetylcholinesterase.
18. Write down a major difference between irreversible and
reversible inhibition.
19. Competitive inhibition can be overcome by
.........................................
20. What are the differences between noncompetitive and
uncompetitive inhibitions?
21. Give an example of a competitive inhibitor.
22. How does concerted model differ from sequential models of
allosteric regulation?
23. Thrombin cleaves the peptide bonds between .................
and .................
24. How do trypsin and chymotrypsin differ in their specificity?
25. What is the condition when the velocity of enzyme-catalyzed
reaction is independent of substrate [S].
26. The denatured enzymes do not exhibit biological activity.
(True/false). Give reasons.
27. What is the relationship between free energy of activation and
the rate of reaction?
28. Active site is a major part of the enzyme volume.
(True/False).
29. How does penicillin interfere with bacterial cell wall
synthesis?
30. What is the difference between a cofactor and a prosthetic
group?
31. Are rate and equilibrium of a reaction independent of each
other? Give reasons.
32. What is the significance of Km?
33. If the change in standard free energy is zero (DGo'=0), how it
will affect the reaction.
34. The amino acids, which constitute an active site should be
together (next to each other) in the linear structure of the protein.
(True/false).
Ch. 8, 11, 12, 13 and 24: Carbohydrate metabolism
1. Glycolysis and citric acid cycle are part of every cell in
human body. (true/false)
2. Name the main regulatory enzyme of glycolytic pathway.
3. Do fructose and galactose enter glycolysis? If yes, what are
the entry
points on the pathway?
4. How does AsO4-3 poisoning affect the ATP production?
5. Where (cellular location) does the conversion of pyruvate into
__________ takes place before it condenses with ________________ to make
citrate? Also write down the number of carbons in each of the intermediates
mentioned in this question.
6. Red blood cells contain the necessary enzymes for both the
glycolysis and the TCA cycle (ture/false).
7. How many ATP molecules are generated only from citric acid
cycle reactions after one molecule of glucose is completely oxidized?
8. Why does the blood level of a-ketoglutarate increase in
Beriberi?
9. How does the inhibition of the phosphofructokinase regulate
hexokinase?
10. How many ATP molecules are generated at the level of electron
transport after oxidation of one glucose molecule?
11. How do NADH and NADPH differ in their function in the cell?
12. ____________________________ is the regulatory enzyme of
pentose phosphate pathway.
13. Glycolysis and pentose phosphate pathways are linked via
______________, ______________________________ and ____________________.
14. How many molecules of NADPH are generated in one cycle of
pentose phosphate pathway?
15. How does GSH (reduced glutathione) link glucose 6-P
dehydrogenase deficiency with primaquin-induced hemolytic anemia? Is primaquin
an antibiotic?
16. The normal human body carries ______ gm. of glucose in
circulation and ________ gm. in the form of _____________, which is sufficient
for about _________ day/s.
17. Why can brain and skeletal muscle not make their own glucose?
18. Gluconeogenesis and glycolysis are reversible and usually run
simultaneously. (true/false) Give reasons.
19. Name the pathway/cycle, which utilizes non-carbohydrate
molecules such as ___________________ for the synthesis of glucose? Why these
molecules have to be transported from some tissues to this tissue _____________
for the synthesis of glucose?
20. The metabolites from pentose phosphate pathway can contribute
to
______________ pathways and the synthesis of
______________________________.
21. Name the enzyme whose deficiency causes galactosemia. What
would you recommend to treat the symptoms of a galactosemic patient?
22. Why does gluconeogenesis take place during exercise even when
glycogen stores are not exhausted?
23. What is the role of mitochondria in gluconeogenesis from
pyruvate?
24. What is the end product of glucose metabolism in the absence
of oxgygen?
25. What are anaplerotic reactions?
26. How does fluoroacetate can arrest TCA cycle and cause death?
27. To drive biosynthetic reactions, which otherwise would be
unfavorable, is the main function of _________________.
28. Why do FADH2 and NADH (TCA) lead to different amount of ATP
generation at e-transport?
29. Why/how can CN and CO poisoning be lethal?
30. What will be the fate of pentose phosphate pathway in a
dividing cell?
31. How does methylene blue help in CN poisoning?
32. What is complex IV in electron transport, how may its
inhibition cause an arrest in the breathing?
33. Measurement of ________________ in the blood serves as a
diagnostic tool to identify the deficiency of _____________ in Beriberi.
34. How will retenone poisoning affect the ATP generation?
35. How does vit B1 deficiency affect carbohydrate metabolism?
36. What are the differences between diabetes type 1 and type 2?
37. Why does glucose transportation is reduced/impaired to muscle
cells in insulin resistance?
38. Why is glycated hemoglobin (HbA1C) a better
measure than blood glucose level of diabetes management?
39. The normal human body carries ______ gm. of glucose in
circulation and ________ gm. in the form of _____________, which is sufficient
for about _________ day/s.
40. What are two enzyme activities of glycogen debranching enzyme?
41. Name the chemical forms of glucose when it is added to and
removed from glycogen. Also write names of the regulatory enzymes involved in
the synthesis and the degradation of glycogen.
42. Glycogen synthase and glycogen phosphorylase are inactive and
active, respectively, when they are _______________________. Write the active
and inactive forms of these enzymes.
43. Epinephrine-mediated increase in cellular cAMP activates an
enzyme ___________________, which leads to the activation of glycogen degradation
but switches of glycogen synthesis at the same time.
44. Insulin stimulates an enzyme _____________, which makes
________________ active and _______________________ inactive through a chemical
reaction called__________________ finally leading to glycogen synthesis or
glycogen breakdown (circle the right choice).
45. What are two significance of glycogenin in the liver?
46. List two diseases along with their clinical symptoms that are
associated with a defect in glycogen phosphorylase.
47. What are the differences between diseases that are associated
with defects in glycogen branching and debranching enzymes?
48. What are the causes and symptoms of Von Gierke's disease.
49. Glycogen degradation does not have to stop before glycogen synthesis
starts. (true/false)
50. How does diabetes lead to neuropathy? How does aldose
reductase play a role in this phenomenon?
51. What are the differences between GLUT 2 and GLUT 4 in their
function, location and sensitivity to insulin?
52. Name the enzyme whose deficiency causes galactosemia. What
would you recommend to treat the symptoms of a galatosemic patient?
53. Glycogen is made of glucose and fructose molecules, which are
joined by a-1,4
linkage? (True/false). If false, describe the correct composition of glycogen.
54. The elevation in blood glucose levels in insulin resistance is
caused mainly by ..................................
55. What is the source of ketone bodies in diabetes?
56. List the long term health consequences of diabetes.
57. What are lectins?
58. N. gonorrhoea infects all human body tissues/cells. Yes or No.
Give reasons.
59. How do N- and O-linked oligosaccharides play a role in the
sperm recognition of the ovulated egg?
60. Cellulose is a polysaccharide made of glucose units, yet it
cannot provide energy if consumed in the diet. Explain. (not covered in the
class)
61. Why is the level of free fatty acids high in the plasma of
diabetic patients?
1. How does plasma differ from serum?
2. An anemic person will be deficient in erythrocytes or leukocytes.
3. How does iron regulate the production of hemoglobin?
4. Why is citrate buffer preferred over other anti-coagulants?
5. RCBs and platelets are not true cells. Explain
6. Name the substance; released from the kidney, that regulates erythrocyte production.
7. List various functions of the albumin.
8. Can a person with Wilson1s disease suffer from anemia?
9. How do transferrin and ceruloplasmin differ from each other? Can the deficiency of ceruloplasmin affect iron metabolism?
10. What is/are common feature(s) between RBC and platelets in terms of structure/function?
11. Of the various blood proteins, which one greatly contributes to the osmotic pressure?
12. What may happen to a person who is diagnosed with low counts of monocytes?
13. Compare and contrast various aspects of ferritin and transferrin.
14. What are immunoglobulins and their function?
15. Invading organisms leads to the production of albumin or hemoglobin or immunoglobin or all of them. (Circle your best answer).
16. A person has higher urinary excretion of Cu2+. Liver biopsy revealed higher concentrations of Cu in the liver. What is your diagnosis? Explain.
17. How does blood fight against invading organisms?
18. What is the correlation between acute phase and C-reactive protein?
19. What is the clinical significance of CRP?
20. What are other proteins released in response to acute phase?
Ch. 4: Oxygen transport
1. Giving the fact that oxygen is soluble in aqueous solutions; the deficiency of hemoglobin can result in death of humans.
2. What is heme and how does it contribute to the function of Hb and Mb?
3. How does heme-Fe++ affects oxygen binding?
4. Binding of first molecule of oxygen does not affect the subsequent binding to the rest of the subunits of Mb or Hb. True/false-explain.
5. Why does CO poisoning occur even at its trace amounts in the air?
6. What makes HbF to bind with oxygen more efficiently than HbA?
7. What does it tell you when Hill coefficient n is greater than 1?
8. You are given Hb and Mb in unlabelled test tubes. How will oxygen-binding experiment help you distinctly recognize these proteins? List at least three characteristics/parameters as a basis to draw your conclusion.
9. You are given HbA and HbF in unlabelled test tubes. How will oxygen-binding experiment help you distinctly recognize these proteins?
10. Other than lower pH, higher CO2 and 2,3-BPG, which factor reduces the oxygen binding to Hb in small capillary beds?
11. What will happen to the Hb sensitivity to 2,3-BPG, if His 243 is replaced with Ser in beta-globin? Explain
12. Increase in the pH, CO2 pressure and 2,3-BPG causes a decrease in Hb affinity with oxygen. Is this a correct statement?
13. Which amino acid is common that participate in pH and CO2-induced reduction in oxygen binding to Hb?
14. Deoxygenated Hb is prone to be protonated-means less affinity for oxygen, yet after delivering of CO2 in the lungs, Hb binds oxygen efficiently in the lungs. Explain.
15. ____________ makes a difference between HbF and HbA in terms of their sensitive to 2,3-BPG.
16. What is the major force of interaction, which helps 2,3-BPG bind with HbA?
17. List chemical and functional differences between normal and sickle cells Hbs.
18. __________ contributes to the polymerization of sickle cell Hb.
19. Of the four structures of proteins discussed in Ch. 2, which one makes a distinction between Hb and Mb?
20. Is Mb present in all human body cells including RBC? Support your answer with reasoning.
21. Do carbon dioxide and oxygen share common binding sites on Hb? Explain.
22. Why is pure oxygen the treatment of choice in CO poisoning?
23. _____________________________ constitute the Bohr effect.
24. In addition to its own effect, CO2 removal contributes to oxygen release from Hb by increasing the concentration of _____________________ as a part of reactions.
25. How p)@ = 60 mmHg and 20mmHg will make a difference in oxygen binding between Hb and Mb?
26. Why may a person die at p02=2- mmHg atmospheric pressure? (P50 for Mb is only 5 mmHg)
27. Other than Hb, ___________________ (enzyme) helps remove CO2 from the body.
Ch. 6: Hemostasis and Thrombosis
1. What is the difference between hemostasis and thrombosis?
2. ________________ is defined as the blocking of blood vessel down stream due to break off the fibrin plug.
3. Release of ________________ and ____________ causes vasoconstriction as a first step in response to bleeding.
4. What is the final step in the process of coagulation?
5. How can the deficiency or excess of vit K affect the coagulation?
6. What are those proteins and/or factors that participate in platelet aggregation and adhesion to vessel wall?
7. Williebrand disease is caused by the deficiency of ______________________.
8. Desmopressin helps release _______________ and thereby treat __________ disease.
9. How are collagen and it C related to the process of hemostasis?
10. Is aspirin used as a procoagulant or anticoagulant drug? Explain your answer in terms of mechanism.
11. What is the clinical usage of warfarin?
12. Hemophilia is caused by the deficiency of ____________________________.
13. List three mechanisms which thrombin acts through to regulate coagulation (a little challenge).
14. What is the molecular role of protein C and protein S in the regulation of coagulation? Explain.
15. ___________________ factor connects coagulation and fibrinolysis.
16. Why does tPA not activate plasminogen while circulating in the blood?
17. Thrombin test is a sure test to diagnose the deficiency of ____________ that can be treated by __________________.
18. What is the end product of fibrinolysis?
Ch. 9, 10: GI, digestion and absorption / Vitamins and minerals
1. What are those three types of macromolecules that need to be digested in the GI tract? And why?
2. Expect __________ and __________, all enzymes released in the GI tract are zymogens.
3. Of the three macromolecules, which one is not broken down (at all) in the mouth?
4. Carbohydrates are absorbed as ____________________.
5. How do maltase and sucrase regulate the osmotic load in the gut?
6. If your diet is completely devoid of sodium, will it affect the absorption of carbohydrates in the enterocyte of the gut? Explain.
7. Arrange the following words/phrases in sequential order to explain the digestion and absorption of fats in the gut: chylomicron, gastric lipase, micelles, bile salts, salivary lipase, TAG, 1- or 2-MAG, fatty acids, apolipoproteins, pancreatic lipase, emulsification. (You may use one word/phrase more than once).
8. What does protect lipase from inactivation by bile salts?
9. How does micelles help lipase digest TAG?
10. List two roles of gastric HC1 in protein digestion.
11. The main role of cholecystokinin is _______________________________.
12. Gastric acid is neutralized in the duodenum by the release of ________________?
13. What is the difference between aminopeptidase and endopeptidase in terms of their action on proteolysis?
14. __________________ is the final product of protein digestion.
15. What are fat-soluble vitamins?
16. Vit A is stored in liver as ___________________.
17. How does vit A deficiency causes night blindness?
18. Vit A has an anticancer activity due to its ______________ property.
19. Can vit A be toxic in adults and teratogenic?
20. How do liver and kidney contribute to the formation of functional vit D?
21. Main function of vit D is _________________________.
22. List the effects of vit D toxicity and deficiency.
23. Despite the fact that your diet has enough vit E, yet you may be vit E deficient. Explain.
24. What is the main function of vit K?
25. Why are pre-term infants more prone to the vit K deficiency?
26. How is vit K produced in your body without the direct involvement of your cellular system?
27. List two effects of vit C being as a reducing agent and an antioxidant.
28. How does vit C contribute to bleeding disorder?
29. List the biological effects of Zn deficiency.
30. Can deficiency of Cu contribute to the oxidative stress/damage? Explain
31. What is the relationship between the excess intake of Cu and the absorption of Zn and Fe? Argue if excessive intake of Cu may cause anemia.
Cell growth, Differentiation and Cancer (Ch 39) and Cyt P450 (Ch 27, pp350-351)
1. What is the difference between oncogenes and proto-oncogenes?
2. What is Go phase of a cell cycle?
3. The difference between G1 and S-phase of a cell includes__________________ ____________________________________________________________..
4. How does apoptosis differ from necrosis?
5. The activation of PLC by growth factor receptors leads to the formation of these two molecules_____________________________________________.
6. Put the sequence of events by which P53 stops the cell going from G1 phase to S-phase.
7. Rb makes a complex with ________________ and thereby regulates cell growth.
8. Describe a relationship between cyclins, CDKs and CDKIs.
9. What are two roles of P53 in cell cycle regulation?
10. Mostly cancer is the result of multiple mutations in a gene. (true/false)
11. How do Bcl-2 prevent apoptosis?
12. What is the role of receptor death domain in apoptosis?
13. What may happen, if a cell is sensed by ________ for it¹s irreparable DNA damage but could not go under apoptosis?
14. What may happen, if ________ is mutated and unable to sense the damage in cellular genome?
15. How does malignant tumor differ from benign tumor?
16. Sarcoma is a cancer of epithelial cells, which is a rare from of cancer. (correct this statement at least in two ways by altering the underlined or bold face words)
17. Ras is an oncogene, which after mutation does not require ______________ for activation and thus becomes constitutively active.
18. What do you measure/determine in a ³Pap smear² test? (self study- box on page 522).
19. Cancer is the result of a highly regulated cellular growth. (false/true)
20. Rb is a negative/positive regulator of cell growth and hence loss of it¹s function will result in the progression/prevention of tumor formation. (circle the underlined or face bold correct words)
21. What are the function/s of p21 and p27?
22. What role do caspases play in apoptosis?
23. What are apoptotic bodies?
24. How do PKCs and MAPKs play role in growth factor signaling and mitogenesis?
25. Is it necessary that a cell after miototic division must enter G1 phase?
26. How do Ras and P53 differ in their roles in mitogenesis and apoptosis?
27. Name two tumor suppressor genes? Do they require mutations in both or one copy for transformations? Give reasons.
28. How will the cell growth be affected in the event of mutations in oncogenes and tumor suppressor genes?
29. What is oncogene collaboration?
30. Cyt P450 is present in almost all cells. (true or false)
31. Why does drug metabolism mainly occur in the liver?
32. How does NADPH-cyt P450 reductase help in hydroxylation of drugs?
33. List three modes of cyt P 450 regulation.
34. What are three-gene families known for metabolizing drugs?
35. Mention the principle behind the fact that cyt P 450 metabolize a vast variety of drugs.
36. How many cyt P450 gene families are known?
37. List the significance of cyt P450.
1. Which of
these statements about the composition of biological membranes is false?
A. The ratio of lipid to protein varies widely among cell types in
a single organism.
B. In a given eukaryotic cell type (say a hepatocyte) all
intracellular membranes have essentially the same complement of lipids and
proteins.
C. The plasma membranes of the cells of vertebrate animals contain
more cholesterol than the mitochondrial membranes.
D. The carbohydrate found in membranes is virtually all part of
either glycolipids or glycoproteins.
2. Which of
these statements about the composition of membranes is generally true?
A. The lipid composition of all membranes of eukaryotic cells is
essentially the same.
B. All biological membranes contain cholesterol.
C. Free fatty acids are major components of all membranes.
D. The inner and outer membranes of mitochondria have different
protein compositions.
3. The inner
(plasma) membrane of E. coli is about 75% lipid and 25% protein by weight. How
many molecules of membrane lipid are there for each molecule of protein?
(Assume that the average protein is Mr 50,000 and the average lipid, 750.)
A. 1
B. 50
C. 200
D. 10,000
E. 50,000
4. Membrane
proteins:
A. are sometimes covalently attached to lipid moieties.
B. are sometimes covalently attached to carbohydrate moieties.
C. are composed of the same 20 amino acids found in soluble
proteins.
D. have all of the properties listed above.
5. Peripheral
membrane proteins:
A. penetrate deeply into the lipid bilayer.
B. can only be released from membranes by detergent treatment.
C. behave like typical soluble proteins when released from
membranes.
D. are generally bound covalently to phospholipid head groups.
6. Which of
these is a general feature of the lipid bilayer in all biological membranes?
A. Polar, but uncharged, compounds readily diffuse across the
bilayer.
B. Individual lipid molecules are free to diffuse laterally in the
surface of the bilayer.
C. Individual lipid molecules in one face (monolayer) of the
bilayer readily diffuse (flip-flop) to the other monolayer.
D. The bilayer is stabilized by covalent bonds between neighboring
phospholipid molecules.
7. The type
of motion least common in biological membranes is:
A. flip-flop diffusion of phospholipid from one monolayer to the
other.
B. lateral diffusion of individual lipid molecules within the
plane of each monolayer.
C. lateral diffusion of membrane proteins in the bilayer.
D. random motion of the fatty acyl side chains in the interior of
the phospholipid bilayer.
8. The fluidity
of the lipid side chains in the interior of a bilayer is generally increased
by:
A. a decrease in temperature.
B. an increase in fatty acyl chain length.
C. an increase in the number of double bonds in fatty acids.
D. the binding of water to the fatty acyl side chains.
9. The
fluidity of a lipid bilayer will be increased by:
A. decreasing the number of
unsaturated positions.
B. increasing the length of the alkyl
chains.
C. increasing the temperature.
D. decreasing the temperature.
10. When a
bacterium such as E. coli is shifted from a warmer growth temperature to a
cooler growth temperature, it compensates by:
A. putting longer-chain fatty acids into its membranes.
B. putting more unsaturated fatty acids into its membranes.
C. increasing its metabolic rate to generate more heat.
D. synthesizing thicker membranes to insulate the cell.
11. An
integral membrane protein will commonly be solubilized by extraction with:
A. a buffer of alkaline or acid pH.
B. a solution of high ionic strength.
C. a chelating agent that removes divalent cations.
D. a solution containing detergent.
E. hot water.
12. What is
the major class of lipids found in the plasma membrane.
13. Which of
these statements is generally true of integral membrane proteins?
A. The domains that protrude on the cytoplasmic face of the plasma
membrane nearly always have covalently attached oligosaccharides.
B. The have channel activity.
C. They undergo constant rotational motion that moves a given
domain from the outer face of a membrane to the inner face and then back to the
outer.
D. They are unusually susceptible to degradation by trypsin.
14. In a few
words, describe hydrophobic "interactions".
15. Which of
these statements about facilitated diffusion across a membrane is true?
A. It can increase the size of a transmembrane concentration
gradient of the diffusing solute.
B. Its rate is limited by the solubility of the transported solute
in the nonpolar interior of the lipid bilayer.
C. A specific membrane protein lowers the activation energy for
movement of the solute through the membrane.
D. It is responsible for the transport of gases such as O2, N2,
and CH3 across biological membranes.
16. Glucose
transport into erythrocytes is an example of:
A.
facilitated diffusion.
B. active transport.
C. symport.
D. antiport.
17. For the
process of solute transport, Kt is:
A. the maximum rate of glucose transport.
B. analogous to Km for an enzyme-catalyzed reaction.
C. analogous to Ka for ionization of a weak acid.
D. proportional to the number of molecules of glucose transporter
per cell.
18.
Facilitated diffusion through a biological membrane is:
A. generally
irreversible.
B. driven by
ATP.
C. driven by
a difference of solute concentration.
D. always
against a concentration gradient.
19. An
electrogenic Na+ transporter:
A. transports Na+ against its concentration gradient.
B. catalyzes facilitated diffusion of Na+ from a region of high
Na+ concentration to one of lower Na+ concentration.
C. must transport both Na+ and its counterion (Cl-, for example).
D. must catalyze an electron transfer (oxidation-reduction)
reaction simultaneously with Na+ transport.
20. The type
of membrane transport that uses ion gradients as the energy source is:
A. primary active transport.
B. simple diffusion.
C. secondary active transport.
D. passive transport.
21. (a) What
kinds of forces or bonds anchor an integral membrane protein in a biological
membrane? (b) What forces hold a peripheral membrane protein to the membrane?
(c) What might one do to solubilize each of the two types of membrane proteins?
22. Using a
simple diagram, explain the differences between integral and peripheral
membrane proteins.
23. (a) List
the major components of membranes. (b) When a preparation of mitochondrial
membranes was treated with high salt (0.5 M NaCl), it was observed that 40% of
the total protein in this preparation was solubilized. What kind of membrane
proteins are in this soluble extract, and what forces normally hold them to the
membrane? (c) What kind of proteins constitute the insoluble 60%, and what
forces hold these proteins in the membrane?
24. Draw the
structure of a biological membrane as proposed by the fluid mosaic model.
Indicate the positions and orientations of phospholipids, cholesterol, integral
and peripheral membrane proteins, and the carbohydrate moieties of
glycoproteins and glycolipids.
25. Surgeons
scrub their hands with detergent before surgery to kill bacteria. Explain how
this works.
26. What is
an amphipathic compound? Explain how such compounds contribute to the structure
of biological membranes.
27. Explain
why the term "fluid" is used to describe the fluid mosaic model of
the biological membrane.
28. The
bacterium E. coli can grow at 20 °C or at 40 °C. At which growth temperature
would you expect the membrane phospholipids to have a higher ratio of saturated
to unsaturated fatty acids, and why?
29. A protein
is found to extend all the way through the membrane of a cell. Describe this
protein in terms of the location of particular types of amino acid side chains
in its structure and its ability to move within the membrane.
30. List two ways a tree might adjust the
components of its cell membranes to keep them as fluid as possible on a cold
winter morning.
31. A plant
breeder has developed a new frost-resistant variety of tomato that contains
higher levels of unsaturated fatty acids in membrane lipids than those found in
standard tomato varieties. However, when temperatures climb above 95 °F, this
frost-resistant variety dies, whereas the standard variety continues to grow.
Provide a likely explanation of the biochemical basis of increased tolerance to
cold and increased susceptibility to heat of this new tomato variety.
32. What is a
hydrophobic compound? Explain why such compounds are generally able to diffuse
across biological membranes without the aid of a specific transport system.
33.
Phospholipids are amphipathic molecules. Show how this property accounts for
the impermeability of biological membranes to polar compounds and ions.
34. Compare
the structure and activity of a membrane transport protein that transports a
polar substance across a membrane with a typical soluble enzyme. How are
transporter and enzyme similar? How are they different?
35. Compare
and contrast symport and antiport. Describe the transport system mediated by
the Na+K+ ATPase.
36. In a few words, describe the
contribution of hydrophobic "interactions" to the stability of biological
membranes.
LIPIDS
1.- Which of the following is not true of
sterols?
A. Cholesterol is a sterol that is commonly found in mammals.
B. They have a structure that includes four fused rings.
C. They are transported as free molecules in the blood.
D. They are precursors of steroid hormones.
E. They are highly soluble in water.
2.
What is the
molecule to which fatty acids are esterified to form triacylglycerols?
3. Describe the dependence of the melting
point of a fatty acid upon (a) chain length and (b) unsaturation; (c) explain
these dependencies in molecular terms.
4. When relatively high concentrations of fatty acids are suspended in water
they form structures known as ________.
5. When relatively high concentrations of
membrane phospholipids are dissolved in water, they form structures known as
________.
6. Define the term
"amphipathic", the types of assemblies amphipathic molecules form in
water, and what are the forces that contribute to the formation of these
structures?
7. Which type of lipid is capable of spontaneously assembling into the bilayer
structure found in biological membranes? What are the forces that drive bilayer
formation?
8. Free fatty acids in the bloodstream are:
A. bound to hemoglobin.
B. present at levels that are independent of epinephrine.
C. carried by the protein serum albumin.
D. freely soluble in the aqueous phase of the blood.
E. nonexistent; the blood does not contain free fatty acids.
9. Lipoprotein lipase acts in:
A. intracellular lipid breakdown of lipoproteins.
B. intestinal uptake of dietary fat.
C. lipoprotein breakdown to supply needed amino acids.
D. hydrolysis of triacylglycerols of plasma lipoproteins to supply fatty acids
to various tissues.
E. none of the above.
10. The role of hormone-sensitive
triacylglycerol lipase is to:
A. hydrolyze lipids stored in the liver.
B. hydrolyze triacylglycerols stored in adipose tissue.
C. hydrolyze membrane phospholipids in hormone-producing cells.
D. synthesize triacylglycerols in the liver.
E. synthesize lipids in adipose tissue.
11. Fatty acids are activated to
acyl-CoAs and the acyl group is further transferred to carnitine because:
A. acyl-CoAs easily cross the mitochondrial membrane, but the fatty acids
themselves will not.
B. fatty acids cannot be oxidized by FAD unless they are in the acyl-carnitine
form.
C. carnitine is required to oxidize NAD+ to NADH.
D. acyl-carnitines readily cross the mitochondrial inner membrane, but
acyl-CoAs do not.
E. none of the above is true.
12. Which of these is able to cross the
inner mitochondrial membrane?
A. fatty acyl-CoA
B. malonyl-CoA
C. acetyl-CoA
D. fatty acyl-carnitine
E. None of the above can cross.
13. If the 16-carbon saturated fatty acid
palmitate is oxidized completely to carbon dioxide and water (via the
b-oxidation pathway and the citric acid cycle), and all of the
energy-conserving products are used to drive ATP synthesis in the
mitochondrion, the net yield of ATP per molecule of palmitate is, in round
numbers:
A. 3.
B. 10.
C. 25.
D. 130.
E. 1000.
14. Which of the following statements
apply (applies) to the b-oxidation of fatty acids?
1. The process takes place in the cytosol of mammalian cells.
2. Carbon atoms are removed from the acyl chain one at a time.
3. Before oxidation, fatty acids must be converted to their CoA derivatives.
4. NADP+ is the electron acceptor.
5. The products of b-oxidation can directly enter the citric acid cycle for
further oxidation.
A. 1, 2, and 3
B. 1, 2, and 5
C. 3 and 5 only
D. 1 and 3 only
E. 4 only
15. The major site of formation of
acetoacetate from fatty acids is the:
A. intestinal mucosa.
B. adipose tissue.
C. liver.
D. muscle
E. kidney.
16. Why is it more efficient to store
energy as lipid rather than as glycogen?
17. The oxidation of acetyl-CoA added to isolated, intact mitochondria is
stimulated strongly by carnitine. Why?
18. For each two-carbon increase in the length of a saturated fatty acid chain,
how many additional moles of ATP can be formed upon complete oxidation of one
mole of the fatty acid to CO2 and H2O?
19. Describe circumstances under which
you would expect to find high concentrations of ketone body in the urine of a
human.
20. What are ketone bodies and why do
they form during fasting?
21. The rate-limiting step in fatty acid synthesis is:
A. formation of acetyl-CoA from acetate.
B. the reaction catalyzed by acetyl-CoA carboxylase.
C. condensation of acetyl-CoA and malonyl-CoA.
D. the reduction of the acetoacetyl group to a b-hydroxybutyryl group.
E. formation of malonyl-CoA from malonate and coenzyme A.
22. Which of these can be synthesized by
plants but not by humans?
A. palmitate (18:0)
B. stearate (20:0)
C. linoleate [18:2(9,12)]
D. pyruvate
E. phosphatidylcholine
23. Cholesterol is synthesized from:
A. acetyl-CoA.
B. malate.
C. oxalate.
D. lipoic acid.
E. choline.
24. Which of these statements about the
regulation of cholesterol synthesis is not true?
A. Insulin stimulates HMG-CoA reductase.
B. High intracellular cholesterol stimulates formation of cholesterol esters.
C. Cholesterol acquired in the diet has essentially no effect on the synthesis
of cholesterol in the liver.
D. Some metabolite or derivative of cholesterol inhibits HMG-CoA reductase.
E. Failure to regulate cholesterol synthesis predisposes humans to
atherosclerosis.
25. In a few words explain why we require
fats in our diets.
26. Fatty acid synthesis and fatty acid breakdown occur by similar pathways.
Describe, very briefly, 3 ways in which the synthetic and breakdown pathways
differ.
27. What are plasma lipoproteins? What is their general role in mammalian
metabolism?
28. Describe the process by which cholesterol esters in the bloodstream enter
cells.
29. Describe (briefly) two classes of genetic defects in humans that could
produce an elevated blood serum cholesterol level.
30. Dietary triglycerols containing
long-chain fatty acyl moieties are digested, absorbed from the small intestine,
and stored in adipose tissue cells. The following processes occur at different
times and sites:
1. Formation of chylomicrons
2. Hydrolysis by hormone-sensitive triaclyglycerol lipase
3. Micellar formation with bile salts
4. Resynthesis from 2-acylglycerols
5. Hydrolysis by lipoprotein lipase
6. Transport in the circulation as free fatty acids bound to serum albumin
The correct order of these events is given by which of the following sequences?
1. 3, 1, 5, 6, 4, 2
2. 3, 4, 1, 2, 6, 5
3. 1, 4, 3, 5, 6, 2
4. 3, 4, 1, 5, 2, 6
5. 1, 4, 5, 6, 2, 3
31. What are membrane rafts?
32. Describe the similarities and differences between chylomicrons, VLDL, LDL
and HDL.
33. How fatty acids are activated for
degradation?
34. What compounds are the major source
of energy in liver and muscle?
35. What compounds are the major source
of energy in erythrocyte and brain?
36. How are fatty acids transported in
blood?
37. Long chain fatty acids are the major
component of storage triglycerides. In which cellular compartment are these
fatty acids activated for degradation? Are they degraded in the same cellular
compartment?
38. What is the importance of the
carnitine shuttle for the degradation of fatty acids in liver?
39. The carnitine shuttle is inhibited
after
A. ingestion of fat rich meals
B. ingestion of carbohydrate-rich meals
C. degradation of glucose to acetyl-CoA
D. accumulation of triglycerides
40. What is the fate of the reduced
nucleotides produced in the degradation of fatty acids?
41. Name some of the alternative pathways
for the acetyl-CoA produced by oxidative degradation of fatty acids.
42. Why a deficient carnitine metabolism
is life threatening?
43. During fasting and starvation, the
liver uses fatty acids as the source of energy for gluconeogenesis. Explain the
mechanism involved.
44. What the liver does with the excess
acetyl CoA that accumulates in fasting or starvation?
45. Explain the usefulness of ketone
bodies.
46. Plasma glucagon activates or inhibits
the degradation of fatty acids? What mechanism is involved?
47. What are essential fatty acids?
48. Is lipogenesis a critical requirement
for humans?
49. High-carbohydrate/low-fat diet
activates or inhibits lipogenesis? What mechanism is involved?
50. In which cellular compartment fatty
acids are synthesized?
51. Why a low intake of cholesterol is
prescribed for gallstones?
52. How cholesterol circulates in blood?
53. What is the role of glucagon in the
synthesis of cholesterol?
54. How statin drugs reduce the synthesis
of cholesterol.
55. By the amount produced, which is the
most important metabolic product of cholesterol?
56. What is the relation between
cholesterol and the family of HEME-containing cytochrome P450 mono-oxygenases?
57. Is it normal to observe an excess of
LDL in blood after fasting? Discuss it.
58. Discuss the process by which
atherosclerosis is produced.
59. What is the major defect in familial
hypercholesterolemia?
60. Describe the function of
phospholipases?
61. What is the difference between
phosphatidylcholine and plasmalogen?
62. Describe a molecule of phospholipid.
63. Describe the composition of ceramide,
glucosylcerebroside, globoside and ganglioside.
64. What are the two major structural
differences between sphingomyelin and phosphatidylcholine?
65. The O, A, and B blood antigens are
A. phospholipids
B. sphingolipids
C. cholesterol products
D. steroid molecules
66. The products of hydrolysis of
phosphatidylcholine by phospholipase A2 are
A. a fatty acid plus 1-acyl lysophosphatidylcholine
B. a fatty acid plus 2-acyl lysophosphatidylcholine
C. two fatty acids plus glycerol 3-phosphocholine
D. two fatty acids plus glycerol 3-phosphate plus choline
E. two fatty acids plus glycerol plus inorganic phosphate plus choline
67. Gangliosides have which of the
following characteristics?
A. They contain sugars and sugar derivatives
B. They contain sialic acid (N-acetylneuraminic acid)
C. They are found in abnormally high concentrated in neural tissues of patients
with Tay-Sachs disease
D. All of the above.
68. All of the following statements
regarding type lla hyperlipidemia (familial hypercholesterolemia) are correct
EXCEPT
A. there is an increased risk of coronary artery disease
B. the serum low-density lipoprotein (LDL) levels are high
C. it is due to a deficiency of LDL receptors in extrahepatic tissues
D. cholesterol synthesis in extrahepatic cells is deregulated
E. it is a rare, recessive, autosomal condition
69. Long-chain fatty acid moieties are
found in which of the following complex lipids?
A. GM2 gangliosides
B. Phosphatidylserine
C. Galactocerebroside
D. Sphingomyelin
E. All of the above
70. Sphingosine formation involves the
A. reaction of palmitoyl coenzyme A with serine
B. reaction of ceramide and cytidine diphosphate-choline
C. action of B-galactosidase on ceramide galactoside
D. action of ceramidase on ceramide
71. Which of the following statements
apply to the b-oxidation
of fatty acids?
A. The process takes place in the cytosol of mammalian cells.
B. Carbon atoms are removed from the acyl chain one at a time.
C. For oxidation, fatty acids must be converted to their malonyl derivatives.
D. b-oxydation is activated by ingestion of carbohydrates.
E. The products of b-oxidation can directly enter the citric acid cycle for
further oxidation.
72.
Anomalous carnitine transporters lead to muscle weakness because
inhibition of
A.
fatty acid
byosynthesis
B.
carbohydrate
degradation
C.
the storage
of lipids
73. Phospholipases A1 and A2
B.
hydrolyse
sphingosine to produce palmitate and serine
C.
hydrolyse
ceramide to produce sphingosine and a fatty acid
D.
only works
with gangliosides
74. After fasting
A.
it is
normal to observe a high level of LDL in blood.
B.
cholesterol
may precipitate in the gall bladder forming ³stones² . This disease is called gallstones.
C.
fatty acid
biosynthesis is activated.
75. Statin drugs reduce high cholesterol
associated problems by
B.
increasing
the production of Apo100
C.
increasing
the affinity of LDL receptors
D.
blocking
the transformation of chylomicrons to LDL
E.
increasing the LDL concentration in blood
76. High cholesterol
A.
inhibits
3-hydroxy 3-methylglutaryl(HMG)-CoA reductase
B.
reduces the
number of LDL receptors in the
membrane
C.
may
precipitate in the gall bladder forming ³stones² . This disease is called gallstones.
D.
may be
transported back to the liver
(overflow pathway) and deposit in the arterial wall leading to
atherosclerosis.
77. Cholesterol is not the precursor of
A.
vitamin D3
(cholecalciferol)
B.
bile acids
C.
steroid
hormones
D.
mevalonate
78. During fast and
starvation, ketone bodies are
A. an efficient source of
energy for muscle and brain
B. accumulated in brain for
the synthesis of cholesterol
C. used for production of
bile acids
D. used for the synthesis and
accumulation of glycogen in muscle
79. De novo synthesis of fatty acids and
triglycerides
A. occurs under conditions of
excess energy intake
B. is stimulated by fasting
and starvation
C. is directly related to the
concentration of ketone bodies in urine
D. is an essential metabolic
process for humans
E. all of the above.
80. Cholesterol
A.
is
an essential component of mammalian cell membranes
B.
plays
a role in the ethiology of cardiovascular diseases
C.
is
a major component of gall stones
D.
is
the precursor of vitamin D
E.
all
of the above
81.Lipoproteins
A.
are
important because they transport fat molecules between different organs and
tissues.
B.
transporting
cholesterol do not have any significant role in the development of
atherosclerosis.
C.
transport
fatty acids from the intestine to peripheral tissues and liver to be used as
the source of energy.
D.
have
a protein component called polyproteins.
E.
all
of the above.
82.
We require
fats in our diets because
A.
they are
used for energy
B.
they are
used to produce essential amino acids
C.
they
contain essential fatty acids
D. they are used to produce carbohydrates
1. The phosphodiester bonds that link adjacent nucleotides in both RNA and DNA:
A. join the 3' hydroxyl of one nucleotide to the 5' hydroxyl of the next.
B. are susceptible to alkaline hydrolysis.
C. are uncharged at neutral pH.
D. always link A with T and G with C.
2. The difference between a ribonucleotide and a deoxyribonucleotide is:
A. ribo- has a pyranose, deoxy- has a furanose.
B. deoxy- lacks an -OH at C-2.
C. ribo- has an extra -OH at C-4.
D. ribo- has the B-configuration at C-1; deoxy- has the A-configuration.
3. In a nucleic acid duplex, cytosine typically base-pairs with:
A. guanine.
B. uracil.
C. thymine.
D. adenosine.
E. inosine.
4. Which of the following deoxyoligonucleotides will hybridize with a DNA containing the sequence (5')AGACTGGTC(3')?
A. (5')TCTGACCAG(3')
B. (5')GAGTCAACT(3')
C. (5')CTCATTGAG(3')
D. (5')GACCAGTCT(3')
E. (5')TCTGGATCT(3')
5. A major component of RNA but not of DNA is:
A. adenine.
B. guanine.
C. cytosine.
D. uracil.
E. thymine.
6. In double-stranded DNA:
A. the two strands are parallel.
B. sequences rich in A-T base pairs are denatured less readily than those rich in G-C pairs.
C. the structure is compatible only with a right-handed (never a left-handed) helix.
D. the two strands have complementary sequences.
E. the sequence of bases has no effect on the overall structure.
7. In the Watson-Crick structure of DNA the:
A. purine content (fraction of bases that are purines) must be the same in both strands.
B. nucleotides are arranged in the A-form.
C. 2'-hydroxyl groups in ribose sometime participate in hydrogen bonding.
D. adenine content of one strand must be equivalent to the thymine content in both the same strand and the complementary strand.
E. two strands are antiparallel.
8. For the oligoribonucleotide pACGUAC:
A. the nucleotide at the 5' end is a pyrimidine.
B. the nucleotide at the 3' end has a phosphate at its 3' hydroxyl.
C. the nucleotide at the 5' end has a phosphate on its 5' hydroxyl.
D. all of the above are true.
E. none of the above is true.
9. Which of the following is not true of all naturally occurring DNA?
A. Deoxyribose units are connected by 3',5'-phosphodiester bonds.
B. The amount of A always equals the amount of T.
C. The ratio A+T/G+C is constant for all natural DNAs.
D. The two complementary strands are antiparallel.
E. Two hydrogen bonds form between A and T.
10. The polymer (5')GTGATCAAGC(3') could form a double-stranded structure with:
A. (5')CACTAGTTCG(3').
B. (5')CACUAGUUCG(3').
C. (5')CACUTTCGCCC(3').
D. (5')GCTTGATCAC(3').
E. (5')GCCTAGTTUG(3').
11. Which of the following is a palindromic sequence?
A. GGATCC
B. GTATCC
C. GAATCC
D. AGGTCC
E. CCTTCC
12. Which of the following is a mirror repeat?
A. GGATCC
B. GTATCC
C. GAATCC
D. AGGTCC
E. CCTTCC
13. In the laboratory, several factors are known to cause alteration of the chemical structure of DNA. Factor(s) likely to be important in a living cell is(are):
A. heat.
B. low pH.
C. UV light.
D. oxygen.
E. both C and D.
14. In living cells nucleotides serve as:
A. precursors for nucleic acid synthesis.
B. enzyme cofactors.
C. intracellular signals.
D. carriers of metabolic energy.
E. all of the above.
15. What is the difference between a nucleoside and a nucleotide?
16. Draw the structures of hydrogen-bonded adenine and thymine.
17. Compounds that contain an aromatic base, a sugar, and a phosphate group are called (a)_________________. Two purines found in DNA are (b)______________ and __________________. A pyrimidine found in all DNA but in only some RNA is (c)_________________. In DNA, the base pair (d)___-___ is held together by three hydrogen bonds; the base pair (e)___-___ has only two such bonds.
18. Draw a DNA sequence containing a six-nucleotide palindrome.
19. Describe briefly what is meant by saying that two DNA strands are complementary.
20. Mouse DNA hybridizes more extensively with human DNA than with yeast DNA. Explain by describing the factor or factors that determine extent of hybridization.
21. Draw the structure of either an adenine-thymine or a guanine-cytosine base pair as found in the Watson-Crick double-helical structure of DNA. Include all hydrogen bonds.
22. In one sentence, identify the most obvious structural difference between A-form (Watson-Crick) DNA and Z-form DNA.
23. Which molecules form the basic structure of a nucleotide.
24. Describe the differences between nucleotide and nucleoside.
25. Describe the differences between nucleotides and deoxynucleotides.
26. Draw the structure of cAMP.
27. What is the difference between the de novo synthesis of nucleotides and the salvage pathway?
28. In a few words, describe the disease caused by accumulation of uric acid, and the treatment for this disease.
29. Why anticancer and antimicrobial drugs are targeted to a reaction in the synthesis of pyrimidines?
30. How come T-lymphocytes with a block in de novo synthesis of nucleotides can survive under resting conditions?
31. Which is more abundant in a living cell: DNA or RNA?
32. What is the meaning of the DNA strands being antiparallel?
33. Is there any special rule that purines and pyrimidines nucleotides pair between them or with each other.
34. Which is the major difference between A- and Z-form of DNA?
35. Genes belong to the middle or the highly repetitive sequences? Explain your answer.
36. What is satellite DNA?
37. The DNA oligonucleotide abbreviated pATCGAC:
A. has an A at its 3' end.
B. has 6 phosphate groups.
C. has a phosphate on its 3' end.
D. has more purines than pirimidines.
38. In the Watson-Crick model of DNA structure (now called B-form DNA):
A. the 5' ends of both strands are at one end of the helix, and both 3' ends are at the other end of the helix.
B. the bases occupy the interior of the helix.
C. a purine in one strand always hydrogen bonds with a purine in the other strand.
D. G-C pairs share two hydrogen bonds.
E. A-T pairs share three hydrogen bonds.
39. The AZT therapy for AIDS involves the incorporation of azido-TTP into the DNA during replication of the viral genome. Azido-TTP blocks further DNA elongation because
A. the 3¹-azido group cannot form a phosphodiester bond with sebsequent nucleoside triphosphates.
B. the reverse transcriptase is disengaged by the presence of the azido group and cannot continue with the synthesis.
C. the azido containing nucleotide cannot serve as template for the synthesis of other DNA strands.
D. the azido group interferes with the base pairing and the two strands of DNA cannot anneal.
E. None of the above.
40. Which of the following statements is false:
A. The nitrogen component of amino acids is removed to be used in other metabolic pathways and the excess is processed in the urea cycle.
B. In a normal healthy diet, the intake of nitrogen containing protein exceeds the requirements of the body metabolism.
C. In higher mammals, the urea cycle produces uric acid, which difusses to the blood and is excreted by the kidney.
D. An excess of uric acid in body fluids may precipitate in soft tissues, particularly in joints. This disease is known as ³gout².
E. None of the above
41. Which of the following statements is true:
A. In higher mammals, proteins are usually degraded and used as a source of energy.
B. Proteins are required as part of the diet.
C. Almost all of the amino acids can be synthesized from the products of degradation of other amino acids, or from carbohydrates and lipids.
D. In a no-carbohydrate diet, products of amino acid degradation are the main source of energy in muscle .
E. None of the above.
42. Some chemotherapeutic agents are used to block pyrimidine biosynthesis because
A. pyrimidines are essential components of DNA. When DNA synthesis is blocked the cells cannot divide.
B. some immune cells (T lymphocytes) use pyrimidines from the salvage pathway. Lack of pyrimidines would block their activation.
C. they block the reduction of dihydrofolate which prevents the synthesis of histidine and methionine.
D. they are very selective reagents that prevent cell division of tumoregenic cells.
E. None of the above.
RNA AND PROTEIN SYNTHESIS
1. Which of the following is not true of the mRNA for ovalbumin?
A. The mRNA is originally synthesized in the nucleus, but ends up in the cytoplasm.
B. The mature mRNA is substantially shorter than the corresponding region on the DNA.
C. Introns are complementary to their adjacent exons and will form hybrids with them.
E. Exons are for polypeptide synthesis.
F. The splicing that yields a mature mRNA occurs at very specific sites in the RNA primary transcript.
2. List one basic property that distinguishes RNA polymerases from DNA polymerases, and list one basic property they share.
3. Write the sequence of the messenger RNA molecule synthesized from a DNA template strand having the sequence:
(5')ATCGTACCGTTA(3')
4. In a certain organism, the gene for hexokinase has 20,000 base pairs. The molecular weight of hexokinase is 100,000. Is the organism likely to be a eukaryote or a prokaryote? Explain your answer.
5. Describe in words (no structures) the important features of the structures present on the 5' and 3' ends of mature (processed) eukaryotic mRNAs.
6. Transfer RNAs have several bases in addition to the normal four found in RNA. How are these rare bases incorporated into the tRNA molecule?
7. A major component of RNA but not of DNA is:
A. adenine.
B. guanine.
C. cytosine.
D. uracil.
E. thymine.
8. RNA polymerase:
A. separates DNA strands throughout a long region of DNA (up to thousands of base pairs), then copies one of them.
B. has a subunit called l (lambda), which acts as a proofreading ribonuclease.
C. binds tightly to a region of DNA thousands of base pairs away from the DNA to be transcribed.
D. can synthesize RNA chains de novo (without a primer).
9. A single base change in a mRNA may result in:
A. no observable mutation.
B. a missense mutation.
C. a nonsense mutation.
D. all of the above.
E. none of the above.
10. Which of the following is not true of tRNA molecules?
A. They contain more than four different bases.
B. The 3'-terminal sequence is -CCA.
C. If the appropriate enzyme is provided, any given tRNA molecule will accept any of the twenty amino acids.
D. They contain several short regions of double helix.
E. None of the above.
11.- Describe different kinds of RNA and their differences.
12.- Describe the differences between the DNA and RNA molecules.
13.- How are RNA molecules synthesized?
14.- Describe three characteristics that differentiate RNA of eukaryotics from prokaryotics.
15.- Do RNA polymerases needs a template? Do they need a primer?
16.- How RNA polymerases identify the correct sequence of DNA they use as template for synthesis of a RNA molecule?
17.- Describe the mechanism of termination of transcription.
18.- What is post-transcriptional processing?
19.- What are promoters?
20. Which of the following is true about the genetic code?
A. It is universal, without exception.
B. Several codons may code for the same amino acid.
C. The base in the middle position of the tRNA anticodon sometimes permits "wobble" base pairing with 2 or 3 different codons.
D. All codons recognized by a given tRNA encode different amino acids.
E. The first position of the tRNA anticodon is always adenosine.
21. Which of the following are features of the wobble hypothesis?
A. A tRNA can read only one codon.
B. Some tRNAs can read codons that specify two different amino acids, although both amino acids are always nonpolar.
C. The third base pair in a codon is always a normal Watson-Crick base pair.
D. The "wobble" occurs only in the first base of the anticodon.
E. A naturally occurring tRNA exists in yeast that can read both arginine and lysine codons.
22. A certain bacterial mRNA is known to represent only one gene and to contain about 800 nucleotides. Assuming that the average amino acid residue contributes 110 to the peptide molecular weight, the largest polypeptide that this mRNA could code for would have a molecular weight of about:
A. 800.
B. 5,000.
C. 30,000.
D. 80,000.
E. It is impossible to set an upper limit with the data given.
23. The mRNA for a polypeptide chain of molecular weight 50,000 has a minimum length of: (Assume that the average amino acid residue contributes 110 to the peptide molecular weight.)
A. 133 nucleotides.
B. 460 nucleotides.
C. 1400 nucleotides.
D. 5000 nucleotides.
E. It is impossible to determine with the data given.
24. Which of the following statements about bacterial mRNA is true?
A. During polypeptide synthesis, ribosomes move along the mRNA in the direction 5' to 3'.
B. An mRNA molecule cannot begin to direct protein synthesis until it is completed, because the point of ribosomal binding for polypeptide initiation is always near the end of the mRNA that is synthesized last.
C. The codon signaling peptide termination should be located in the mRNA near the 5' end.
D. Once synthesized by the bacterium this mRNA is never degraded, but is passed on to the daughter cells at cell division.
25. Which of the following statements about tRNA molecules is false?
A. There is at least one tRNA for each of the 20 amino acids.
B. The amino acid attachment is always to an A nucleotide at the 3' end of the molecule.
C. Any given tRNA will only accept one specific amino acid.
D. A, C, G, and U are the only bases present in the molecule.
E. Although composed of a single strand of RNA, each molecule contains several short, double-helical regions.
26. Which of the following statements about the tRNA that normally accepts phenylalanine is false? (The mRNA codon for phenylalanine is UUU.)
A. It contain modified bases in its molecule.
B. Phenylalanine can be specifically attached to an -OH group at the 3' end.
C. The tRNA must contain the sequence UUU.
D. It will accept only the amino acid phenylalanine.
E. When coupled to phenylalanine, it can bind to the "A" site on ribosomes.
27.- What is a polycystronic mRNA?
28. Which of the following statements about aminoacyl-tRNA synthetases is false?
A. There is a different synthetase for every amino acid.
B. The enzyme attaches an amino acid to the 3' end of a tRNA.
C. The enzyme splits ATP to AMP + PPi.
D. The enzyme will use any tRNA species, but is highly specific for a given amino acid.
E. Some of the enzymes have an editing/proofreading capacity.
29. Aminoacyl-tRNA synthetases (amino acid activating enzymes):
A. "recognize" specific tRNA molecules and specific amino acids.
B. interact directly with free ribosomes.
C. in conjunction with another enzyme attach the amino acid to the tRNA.
D. require GTP to activate the amino acid.
E. have all the properties listed above.
30. In E. coli, aminoacyl-tRNA synthetases:
A. require a tRNA, an amino acid, and GTP as substrates.
B. are amino acid-specific; there is at least one enzyme specific for each amino acid.
C. activate amino acids in twelve steps.
D. have no proofreading activities.
E. fall into two classes, which attach amino acids to different ends of the tRNA.
31. Which of the following statements about ribosomes is true?
A. There are two major subunits, each with multiple proteins.
B. They are relatively small, with molecular weights less than 10,000.
C. The large subunit contains rRNA molecules, the small subunit does not.
D. There are about 25 of them in an E. coli cell.
E. The RNA in ribosomes plays a structural, not catalytic, role.
32. It is possible to convert the Cys that is a part of Cys-tRNACys to Ala by a catalytic reduction. If the resulting Ala-tRNACys were added to a mixture of ribosomes, all the other tRNAs and amino acids, all of the cofactors and enzymes needed to make protein in vitro, and mRNA for hemoglobin, where in the newly synthesized hemoglobin would the Ala from Ala-tRNACys be incorporated?
A. wherever Ala normally occurs
B. wherever Cys normally occurs
C. wherever either Ala or Cys normally occurs
D. wherever the dipeptide Ala-Cys normally occurs
E. nowhere; this is the equivalent of a nonsense mutation
33. Which of the following is true about the sorting pathway for proteins destined for incorporation into lysosomes or the plasma membrane of eukaryotic cells?
A. The newly synthesized polypeptides include a leader peptide at their carboxyl termini.
B. The signal recognition particle (SRP) binds to the leader peptide soon after it appears outside the ribosome.
C. Binding of SRP to the leader peptide and the ribosome temporarily accelerates protein synthesis.
D. The leader peptide is cleaved off inside the mitochondria by signal peptidase.
E. The signal sequence is added to the polypeptide in a posttranslational modification reaction.
34. You have isolated a fragment of viral DNA that totally encodes at least two proteins, 120 and 80 amino acids long. The DNA fragment is 400 base pairs long. (a) Why might you consider this unusual? (b) Propose two models to account for this, one of which you might be able to rule out if you sequence the two proteins. (c) You sequence the two proteins and find no sequence homology. Which proposal does this rule out? Why?
35. The template strand of a segment of double-stranded DNA contains the sequence:
(5')CTT TGA TAA GGA TAG CCC TTC
A. What is the base sequence of the mRNA that can be transcribed from this strand? (b) What amino acid sequence could be coded by the mRNA base sequence in (a), using only the first reading frame starting at the 5' end? (Refer to the genetic code table.) (c) Suppose the other (complementary) strand is used as a template for transcription. What is the amino acid sequence of the resulting peptide, again starting from the 5' end and using only the first reading frame?
36. A given DNA sequence might be read in any of three reading frames. Describe two ways that (a) prokaryotes and (b) eukaryotes determine the correct reading frame.
37. Polypeptide chain elongation in E. coli occurs by the cyclical repetition of three steps. What are these steps and what cellular components are necessary for each of them to occur?
38. Indicate whether each of the following statements is true (T) or false (F).
___ Messenger RNA is broken down within a few minutes of its formation
in E. coli.
___ Messenger RNA is never longer than the DNA of a single structural
gene.
___ Polysomes do not necessarily contain mRNA.
___ Messenger RNA normally occurs as a double-stranded helix, with one
strand containing codons, the other containing anticodons.
___ Messenger RNA contains the information that codes for tRNA
synthesis on the ribosome.
39. Indicate whether the following statements are true (T) or false (F).
___ A ribosome is the complex within which protein synthesis occurs.
___ Ribosomes contain many separate proteins.
___ The three ribosomal RNAs in a bacterial ribosome are distributed in three separate large ribosomal subunits.
___ There are four binding sites for tRNAs on a ribosome.
40. A new antibiotic named ericamycin was recently discovered by a brilliant graduate student. This antibiotic works by inhibiting prokaryotic protein synthesis. In the presence of ericamycin protein synthesis can initiate, but only dipeptides that remain bound to the ribosome are formed. What specific step of protein synthesis is likely to be blocked by this antibiotic?
41. Place the following steps (1-4) in the proper order with regard to protein synthesis.
___ Peptide bond formation shifts the growing peptide from the P to
the A site.
___ Charged tRNA binds to the A site.
___ The 50S subunit binds to the initiation complex of the 30S subunit
and mRNA.
___ Uncharged tRNA is released from ribosome.
42. When first synthesized, proinsulin has an additional leader or signal peptide at its amino terminus. This complete molecule is preproinsulin and the leader sequence is cleaved off to give proinsulin. Briefly, what is the function of the leader peptide?
43. Describe the sequence of events between the transcription of mRNA for a secreted protein and the arrival of that protein in the lumen of the endoplasmic reticulum.
44.Which of the following statements is true.
A. Aproximately 90% of the nucleic acid within cells is RNA.
B. DNA is composed of nucleotides containing the sugar deoxyribose.
C. The structure of DNA was originally proposed by Watson and Crick.
D. In the DNA structure, each guanine can form three hydrogen bonds with cytosine.
E. All of the above
45.- During transcription
A. RNA molecules are synthesized using DNA as a template
B. aminoacyl-tRNA binds to the acceptor site
C. the processes of initiation, elongation and post-translational modification take place
D. DNA polymerase binds to the promoter region
E. All of the above
46.- Which of the following statements related to promoters is true.
a) Promoters are specific sequences of DNA, usually located in front (upstream) of the gene that is to be transcribed.
b) Promoters in eukaryotic cells are simpler than prokaryotics.
c) Response elements are part of the promoters
d) Transcription factors bind to promoters during elongation
e) All of the above
47.- Post-transcriptional processing includes
A. removal of sequences from the primary transcript
B. modification of bases
C. addition of more nucleotides
D. all of the above
E. none of the above
48.- One characteristic that distinguish eukaryotic from prokaryotic mRNA is
A. that single eukaryotic mRNAs encode multiple proteins (polycistronic).
B. that prokaryotic mRNA has introns
C. that eukaryotic mRNA has large non-coding sequences inserted between the coding sequences and they must be removed before protein synthesis takes place.
D. that prokaryotic mRNA has a 3¹-cap and a 5¹-polyA tail.
E. None of the above.
49.- One characteristic postralational modification of proteins involves
A. the substitution of the first methionine of the just synthesized protein by another amino acid.
B. the addition of a poly-A tail
C. the addition of a fatty acid to the c-terminal end
D. removal of the signal sequence
E. None of the above
50.- During the initiation process of protein synthesis
a) a tRNA molecule binds to the P site, and then amino acyl-tRNA synthesize binds the corresponding amino acid
b) the ribosome subunits assemble on the mRNA and the P site is occupied by a methionyl-tRNA molecule.
c) The interaction of a ribosomal RNA sequence with the mRNA promoter region localizes the P-site of the ribosome just at the beginning of the coding sequence
d) Initiation factors interact with the promoter region of the mRNA to form the initiation complex
e) None of the above
51.- A striking characteristic of peptidyl transferase is
A. that uses GTP instead of ATP to produce the peptide bond
B. that it is not a protein
C. that it has fatty acids covalently attached to two aspartic acid residues located close to the C-terminal end of the protein
D. that the cofactors of the reaction bind to a rRNA molecule attached to the enzyme
E. none of the above
52.- The genetic code is degenerate because
A. there is more than one codon per amino acid
B. the 3¹ base of the codon can form nonclassical base pairs
C. of the wobble hypothesis of codon-anticodon
D. there is more than one anticodon per tRNA
E. none of the above
53.- The ribosome knows where to start protein synthesis because
A. of the interaction of the Shine-Delgarno sequence with a sequence of the 16S bacterial rRNA
B. of the interaction of the mRNA promoter with a sequence of the 16S bacterial rRNA
C. of the interaction of the poly-A tail with a sequence of the 16S bacterial rRNA
D. of the interaction of a Zn-finger sequence with a sequence of the 16S bacterial rRNA
E. none of the above
CONTROL OF GENE EXPRESSION
1. Which of the following statements correctly describes promoters in E. Coli?
A. All promoters have the same sequence, which is recognized by RNA polymerase.
B. Every promoter has a different sequence, with little or no resemblance to other promoters.
C. Many promoters are similar and resemble a consensus sequence, which has the highest affinity for RNA polymerase.
D. A promoter may be present on either side of a gene or in the middle of it.
E. Promoters are not essential for gene transcription, but they can increase transcription by two- to threefold.
2. The rate of transcription initiation in bacteria is influenced by:
A. the composition of the leading sequence.
B. repressors.
C. activators.
D. B and C.
E. none of the above.
3.- Describe the following terms.
____ leucine zipper
____ activator
____ zinc finger
____ repressor
____ helix-turn-helix
4.- The enzyme liverase is found only in the liver of mice (i.e., the enzyme is not found in any other organ such as spleen). However, you find that the gene encoding this enzyme is transcribed at equal rates in liver and spleen cells. By defining the level of liverase gene expression as the level of enzyme in the cell, list three points at which expression of the liverase gene might be differentially regulated in liver and spleen cells.
5.- Can RNA polymerase initiate transcription alone?
6.- Promoters
A. act as a basic recognition unit, signaling that there is a gene nearby that can be transcribed.
B. are a domain of amino acids found upstream of the DNA initiation site.
C. are the same for all genes.
D. are not used for expression of 50% of the genes.
E. all of the above.
7.- Which is not a common component of promoters:
A. TATA box
B. CAAT box
C. GC box
D. Response element sequence
E. B and D
8.- A motif not found in the DNA-binding regions of proteins is:
A. helix-turn-helix
B. helix-loop-helix
C. zinc finger
D. leucine zipper
E. double-helix turn
9.- Which of the following statements is true:
A. During transcription, protein leucine zipper motives separate DNA double strands to facilitate the binding of the RNA polymerase.
B. Transcription may proceed without the participation of any transcription factor.
C. For the transcription of immnunoglobulin genes, transcription factors may bind to enhancers sequences present within an intron of the gene being transcribed.
D. Mutations in enhancers may not affect transcription efficiency.
E. All of the above.
10.- Which of the following statements are true (it may be more than one)
A. Each gene has response element sequences.
B. RNA editing may involve the insertion, deletion, or substitution of nucleotides in the RNA molecule.
C. Paternal and maternal copies of the gene are normally expressed from autosomal chromosomes.
D. By alternative splicing, different tissues may express different proteins from the same original mRNA.
E. The DNA-binding region of steroid hormone receptors always contains a zinc finger region which, if mutated, results in loss of function of the receptor.
11.- Describe the molecular mechanism by which steroid hormones may modify gene expression.
12.- Describe genomic imprinting.
13.- Describe an example of mRNA alternative splicing.
14.- Which of the following statements is not true:
A. The nucleotide sequence of the start point of a gene varies from gene to gene.
B. The "TATA" box is relatively fixed approximately 25 bp from the start point.
C. All genes possess response elements.
D. After transcription starts, many of the transcription factors are released.
E. A protein known as TATA-binding protein (TBP) binds to the TATA box.
15.- Which of the following statements is not true:
A. Differential splicing may produce tissue-specific mRNA molecules that are translated into tissue-specific proteins.
B. All genes are biallelic.
C. ApoB 100 and ApoB 48 are produced from the same original mRNA.
D. None of the above.
MEMBRANE RECEPTORS AND SIGNAL TRANSDUCTION
1.- Second messengers are
A. alternative hormones
B. G-protein binding molecules
C. Lipid molecules
D. Intracellular signaling molecules
E. None of the above
2.- Receptors for steroid hormones can be
A. directly linked to cAMP
B. transcription factors
C. attached to the intracellular face of the plasma membrane
D. enzymes that phosphorylate tyrosine residues
E. none of the above
3.- Why specific differential sets of responses are induced by the same steroid hormone when it bind to the same receptor in different cells.
4.- Describe the mechanism of activation/deactivation of G-proteins during receptor signaling.
5.- G-proteins are activated by
A. tyrosine phosphorylation of the beta-subunit
B. nitric oxide binding to the gamma-beta complex
C. binding of GTP to the alpha-subunit
D. degradation of the GDP bound to the alpha-subunit
E. none of the above
6.- Some of the G-protein coupled receptors are deactivated (desensitized) by
A. amination of the GDP-binding carboxyl
B. deamination of the GDP-binding carboxyl
C. phosphorylation of a tyrosine residue at the hormone binding site
D. phosphorylation of the C-terminal tail by a kinase
E. all of the above
7.- Which of the following statements are true
A. The G-protein subunits dissociate after binding of GTP to the alpha-subunit.
B. Only the alpha-subunit can transduce the signal generated by the binding of the hormone to the receptor.
C. The GTP bound to the alpha subunit is hydrolyzed to GDP plus Pi by a soluble cytosolic phosphatase.
D. cAMP is produced from ATP by the GTP-alpha subunit complex.
E. Phosphodiesterases can migrate to the nucleus and activate gene expression after binding to the activated G-protein.
8.- Explain how the binding of a few hormone molecules to beta-adrenergic receptors may result in the release of a large number of sugar molecules.
9.- Diacylglycerol (DAG)
A. can be produced by degradation of phosphatidylcholine
B. can be produced by degradation of phosphatidylinositol
C. can activate protein kinase C
D. can activate cAMP
E. can activate protein kinase A
10.- Arachidonic acid
A. is generated from phosphatidylcholine by PLA2
B. is the precursor of prostaglandins
C. is the precursor of tromboxanes
D. is a fatty acid with four unsaturated bonds
E. all of the above
11.- Aspirin and Ibuprofen reduce inflammation and pain by
A. blocking the cyclo-oxygenase pathway from arachidonic acid
B. blocking the lipoxygenase pathway from arachidonic acid
C. blocking the production of leukotrienes
D. blocking PLA2 activity
E. none of the above
12.- Eicosanoids are
A. prostaglandins
B. prostacyclins
C. tromboxanes
D. leukotrienes
E. all of the above
13.- DAG fulfils its second messenger role by activating the key signaling enzyme
A. adenylate cyclase
B. phosphodiesterase
C. PKA
D. PKC
E. Inositol 3-phosphate kinase
14.- Which of the following statements is not true
A. Phosphodiesterases terminate the cAMP signal by converting cAMP to its 5'AMP metabolite.
B. PKA is a multimeric enzyme comprising two regulatory and two catalytic subunits.
C. Dibutyryl-cAMP, a cell membrane permeant analog of cAMP can mimic the effects of hormones that induce glycogen breakdown.
D. G-protein alpha-subunit has an intrinsic GTPase activity.
E. G-protein coupled receptors are proteins characterized by the nine transmembrane-spanning helices within their structure.
15.- How NO can modulate the activity of cytoplasmic signal-transducing enzymes?
16.- Explain how the signal originated by the binding of the hormone to the receptor is amplified by the second messengers.
17.- Describe the components of the signaling cascade involved in the regulation of glycogen metabolism.
18.- Which of the following statements are true
A. Binding of calcium induces a conformational change that allows calmodulin to bind to and regulate target proteins.
B. Calmodulin is a subunit of phosphorylase kinase.
C. PIP2 is hydrolyzed by PLC to generate two second messengers: IP3 and DAG.
D. IP3 is a water soluble molecule that mobilizes intracellular stores of calcium.
E. All of the above.
19.- Which of the following statements are true
A. IP3 is very stable after synthesis and remains at relative high concentration in the cytosol.
B. IP3 binds to specific receptors on the ER to release calcium
C. The synthesis of IP3 is directly linked to the level of cellular cAMP.
D. IP3 can re-link to DAG to form PIP2.
E. IP3 binds to calmodulin to activate phosphorylase kinase.
20.- Which of the following statements are true
A. Calcium, phospholipids and DAG are activators of classical PKC molecules.
B. Under basal conditions, the pseudosubstrate domain of the PKC molecule interacts with the substrate-binding domain and represses PKC activity.
C. PKC activation is associated with translocation from the cytosol to the plasma or nuclear membranes.
D. While PKA only phosphorylates serine and threonine residues, PKC phosphorylates serine, threonine and tyrosine residues of proteins.
E. None of the above.
21. The largest energy store in a well-nourished human is:
A. muscle glycogen.
B. liver glycogen.
C. blood glucose.
D. triacylglycerols in adipose tissue.
E. ATP in all tissues.
22. Skeletal muscle uses _________ as an energy source.
A. fatty acids
B. ketone bodies
C. glucose
D. proteins
E. all of the above
23. An energy source generally not used by brain tissue is:
A. fatty acids.
B. glucose.
C. ketone bodies.
D. None of the above.
E. All of the above are used as fuels.
24. Which of the following statements is true?
A. The brain prefers glucose as an energy source, but can use ketone bodies.
B. Muscle cannot use fatty acids as an energy source.
C. In a well-fed human, about equal amounts of energy are stored as glycogen and as triacylglycerol.
D. Fatty acids cannot be used as an energy source in humans, because humans lack the enzymes of the glyoxylate cycle.
E. None of the above
25. Which of these is not a normal component of human blood?
A. erythrocytes
B. LDL (low-density lipoproteins)
C. prothrombin
D. immunoglobulins
E. All of the above are found in blood.
26. Elevated epinephrine levels do not normally stimulate:
A. glycogen breakdown in muscle.
B. glycogen synthesis in liver.
C. gluconeogenesis in liver.
D. glycolysis in muscle.
E. fatty acid mobilization in adipose tissue.
27. When blood glucose is abnormally low, the pancreas releases:
A. insulin.
B. glucagon.
C. epinephrine.
D. trypsin.
E. glucose.
28. When blood glucose is abnormally high, the pancreas releases:
A. insulin.
B. glucagon.
C. epinephrine.
D. trypsin.
E. glucose.
29. An elevated insulin level in the blood:
A. results from a below-normal blood glucose level.
B. inhibits glycogen synthesis in liver and muscle.
C. stimulates synthesis of fatty acids and triacylglycerols in liver.
D. inhibits glucose uptake by liver.
E. stimulates glycogen breakdown in liver.
30. The sequence of events in the response of hepatocytes to elevated epinephrine is:
1. GTP replaces GDP on Gs
2. adenylate cyclase is activated
3. epinephrine binds to its receptor on the cell surface
4. Gs associates with adenylate cyclase
5. cAMP-dependent protein kinase is activated
A. 2, 4, 1, 3, 5
B. 3, 1, 4, 2, 5
C. 3, 2, 1, 4, 5
D. 3, 5, 4, 2, 1
E. 5, 2, 3, 1, 4
31. The sequence of events in the response of hepatocytes to elevated insulin is:
1. the tyrosine kinase domain of insulin receptor is
autophosphorylated
2. insulin binds to the a subunit of the receptor
3. the tyrosine kinase domain phosphorylates (a) tyrosine
residue(s) on the target protein(s).
A. 1, 2, 3
B. 2, 1, 3
C. 2, 3, 1
D. 3, 1, 2
E. 3, 2, 1
32. When inositol-1,4,5-trisphosphate (IP3) binds to its specific receptor:
A. a phospholipase in the plasma membrane is activated.
B. Ca2+ is released from the endoplasmic reticulum into the cytosol.
C. GTP replaces GDP on a Gs protein.
D. the intracellular concentration of cAMP rises.
E. There is no intracellular receptor for IP3.
33. What distinguishes eicosanoids from other potent biological signaling molecules such as epinephrine?
34. Describe the sequence of biochemical events between the release of epinephrine into the bloodstream and the activation of the enzyme glycogen phosphorylase.
35. The toxins produced by Bordetella pertussis (which causes whooping cough) and by Vibrio cholerae (which causes cholera) have similar modes of action in toxin-sensitive mammalian cells. Describe the molecular basis for their toxic effects.
36. A number of proteins are known to be activated by phosphorylation catalyzed by specific protein kinases, responsive to extracellular signals. When the signals cease, the phosphorylated proteins do not remain active forever. What accounts for their inactivation?
37. Explain how amplification of a hormonal signal takes place; illustrate with a specific example.
38. Explain how amplification occurs in signal transductions, with examples from two of these systems: the b-adrenergic receptor, the insulin receptor, or the vasopressin system via inositol-1,4,5-trisphosphate (IP3).
39. Compare and contrast the modes of action of epinephrine, acting through the b-adrenergic receptor, and of insulin, acting through the insulin receptor.
40. GTP-binding proteins play critical roles in many signal transductions. Describe two cases in which such proteins act, and compare the role of the G proteins in each case.
41. The receptors for steroid hormones and thyroid hormones are strikingly similar in structure. Explain, in terms of the structure of the receptor and the hormone response element (HRE), how a certain receptor is able to (a) respond only to a given steroid hormone, and (b) change the transcription of only specific genes.
42. Signals carried by hormones must eventually be terminated; the response continues for a limited time. Discuss three different mechanisms for signal termination, using specific systems as examples.
43. Explain how mutations in the following proteins might result in either loss of responsiveness to a given hormone or production of a continuous signal even in the absence of the hormone: (a) a mutation in the regulatory (R) subunit of cAMP-dependent protein kinase, making R incapable of binding to the catalytic (C) subunit; (b) a mutation in a protein-tyrosine phosphatase; (c) a defect in a G protein that renders the GTPase activity inactive.
=====================================================
NEWLY ADDED PROBLEMS:
Essential amino acids
a. cannot be derived from normal human metabolism.
b. are also known as ³ketogenic amino acids².
c. can only be synthesized from ketone bodies.
d. are not required in the diet.
e. have none of the above features.
Describe the various levels of structure by which the DNA is compacted more than 8,000 fold to fit into the nucleus.
Phenylketonuria is an inborn error of metabolism resulting from a deficiency of the enzyme
a. phenylalanine hydroxylase.
b. tyrosinase.
c. tyrosine hydroxylase.
d. phenylpyruvate synthase.
e. all of the above.
Describe the function of telomerase. Explain the hypothesis that the somatic cell lacks of telomerase is related to cellular senescence and aging.
6. Gout
a. is produced by precipitation of uric acid and its urate salts (forming ³stones²) in gall bladder.
b. is treated with allopurinol, an inhibitor of xanthine oxidase.
c. results from the precipitation of cholesterol in soft tissues, particularly in joints.
d. is treated with statin-drugs accompanied by a low cholesterol diet.
e. has none of the above features.
7. Which of the following statements is wrong:
a. Organisms with a block in the ³de novo² nucleotide biosynthetic pathways can survive and grow if a source of nucleotides is available from the diet.
b. In humans, almost 60% of the ammonia derived from amino acid catabolism is excreted in urine as uric acid.
c. Resting T lymphocytes meet their requirement for nucleotides through the salvage pathway.
d. In HIV infected but asymptomatic patients, resting lymphocytes have a block in ³de novo² pyrimidine biosynthesis, and correspondingly reduced pyrimidine pool sizes. Following activation , T-lymphocytes cannot synthesize sufficient new DNA and this leads to cell death.
e. All of the above.
What are the roles of the different DNA polymerases during DNA replication?
Besides being used to produce energy, carbons from amino acids may be used for the production of other molecules like ___, ___, ___.
13. Which of the following statements is wrong:
a. Satellite DNA may participate in the alignment of chromosomes during cell division.
b. Mitochondrial DNA is small, circular, and encodes some (but not all) of the mitochondrial proteins.
c. Telomeres consist of G-rich tandem repeats of short, species-specific oligonucleotides, found in the middle of the chromosomes.
d. Histones are a highly conserved family of proteins that are involved in the packing and folding of DNA within the nucleus.
e. None of the above.
14. Which of the following statements is wrong:
a. In the native chromosome, DNA form complexes with RNA and proteins. These DNA-RNA-protein complexes are called chromatin.
b. Somatic cells lack telomerase activity. Because of this, each round of chromosome replication results in chromosome shortening.
c. Nucleosomes are formed by several histones encircled with about 200 bases pairs of DNA that form two coils around the nucleosome core.
d. DNA damage produced by single base substitutions cannot be repaired and cells containing this damaged DNA enters in apoptosis (cell death).
e. None of the above.
15. For cells to divide, their DNA must be duplicated. Which of the following statements related to DNA synthesis is wrong:
a. For DNA replication, the two DNA strands are separated and both of them serve as templates for the synthesis of new strands.
b. DNA synthesis is ³semiconservative² because after each cycle of replication daughter DNA molecules contain one parental strand and one newly synthesized strand.
c. During DNA replication, DNA polymerase adds nucleotides to the 3¹-end of the elongating DNA strands.
d. Instead of a long continuous DNA strand, DNA polymerase III reproduces the leading strand in small fragments called ³Okazaki fragments².
e. None of the above.
What is the object of the urea cycle? Which is the final product? What is it used for?
Describe the process by which antimicrobial and anticancer drugs interfere with the synthesis of pyrimidines.
Folic acid analogs inhibit the synthesis of TTP. Do these drugs also interfere with the synthesis of purine bases?
What is the function of the various DNA polymerases during transcription?
Describe the mechanism of auction of cholera toxin, diphtheria toxin, pertussis toxin, caffeine, and aspirin.
During the synthesis of thymidine triphosphate (TTP), which is actually a deoxy nucleotide, dUTP is produced. DNA polymerase does not effectively discriminate between dUTP and TTP. However, this is not a problem because
a. the incorporated dUTP is transformed (after incorporation) in TTP by DNA polymerase-2.
b. cells limit the concentration of dUTP by rapidly hydrolyzing dUTP to dUMP.
c. DNA polymerase-1 incorporates IMP in the site corresponding to TTP, and after incorporation, DNA polymerase-2 replaces the IMP by TMP.
d. dUTP is maintained in a different cellular compartment from the one that TTP and DNA polymerase are.
e. None of the above.
Activation of steroid receptors leads to protein synthesis. Is this also a possibility for G-protein coupled receptors? What may be the mechanism?
Caffeine induces the cellular accumulation of cAMP by
a. binding to the b-adrenergic receptor, because caffeine can substitute for epinephrine.
b. ADP-ribosylation of an arginine residue on the a-subunit of Gs, which inhibits the GTPase activity.
c. ADP-ribosylation of a serine residue on the a-subunit of adenylate cyclase, which keeps this enzyme in an activated state.
d. inhibition of phosphodiesterase. In this condition, the enzyme cannot degrade cAMP, which accumulates in the cell.
e. None of the above.
Mention five processes in which calcium is involved as second messenger.